Modulome

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.9.dev0

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Modulome
        Analysis of public microbial RNA-seq data

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Contact E-mail
        avsastry@ucsd.edu
        Application Type
        Microbial RNA-seq Analysis

        Report generated on 2020-09-06, 13:00 based on data in: /home/anand/Documents/modulome/modulome-nextflow/aws_results


        General Statistics

        Showing 323/323 rows and 9/10 columns.
        Sample Name% AssignedM Assigned% AlignedM Aligned% BP Trimmed% Dups% GCLengthM Seqs
        SRX063252
        4.4%
        0.7
        64.9%
        9.8
        4.1%
        87.4%
        49%
        31 bp
        15.2
        SRX063253
        0.3%
        0.1
        3.7%
        0.7
        3.7%
        85.9%
        38%
        41 bp
        20.2
        SRX063254
        0.3%
        0.1
        3.5%
        0.7
        3.7%
        86.1%
        38%
        41 bp
        20.2
        SRX1652180
        1.5%
        SRX1655390
        27.6%
        SRX1655391
        1.4%
        SRX1655392
        26.6%
        SRX1655393
        1.5%
        SRX1655394
        27.1%
        SRX2356912
        7.5%
        0.8
        97.0%
        10.0
        0.9%
        95.0%
        55%
        50 bp
        10.3
        SRX2356913
        5.6%
        0.5
        97.1%
        8.5
        1.0%
        95.7%
        55%
        50 bp
        8.7
        SRX2356914
        5.9%
        0.6
        96.8%
        9.6
        0.9%
        95.7%
        55%
        50 bp
        9.9
        SRX2356915
        4.4%
        0.5
        96.6%
        11.2
        0.9%
        96.4%
        54%
        50 bp
        11.6
        SRX2356916
        3.6%
        0.3
        97.1%
        8.2
        1.0%
        96.3%
        54%
        50 bp
        8.5
        SRX2356917
        2.9%
        0.3
        96.9%
        10.6
        0.9%
        96.7%
        54%
        50 bp
        10.9
        SRX2356918
        2.0%
        0.2
        96.8%
        10.1
        1.0%
        96.9%
        54%
        50 bp
        10.4
        SRX2356919
        1.6%
        0.3
        97.2%
        17.9
        0.9%
        97.4%
        54%
        50 bp
        18.4
        SRX2356920
        1.6%
        0.2
        96.0%
        13.0
        1.0%
        96.7%
        54%
        50 bp
        13.5
        SRX2356921
        5.7%
        0.5
        95.7%
        9.1
        1.5%
        93.7%
        55%
        49 bp
        9.5
        SRX2356922
        8.4%
        1.0
        95.0%
        11.8
        1.2%
        93.5%
        55%
        49 bp
        12.4
        SRX2356923
        8.3%
        1.0
        95.9%
        11.0
        1.0%
        94.3%
        55%
        50 bp
        11.5
        SRX2356924
        9.4%
        1.1
        97.5%
        11.1
        1.1%
        94.0%
        55%
        49 bp
        11.4
        SRX2356925
        7.5%
        0.8
        97.5%
        10.9
        1.1%
        94.8%
        55%
        49 bp
        11.2
        SRX2356926
        6.5%
        0.9
        97.1%
        13.9
        1.2%
        93.9%
        55%
        49 bp
        14.3
        SRX2356927
        6.6%
        0.8
        97.2%
        11.2
        1.1%
        94.9%
        54%
        49 bp
        11.5
        SRX2356928
        5.4%
        0.7
        97.6%
        12.8
        1.1%
        95.1%
        54%
        49 bp
        13.1
        SRX2356929
        4.5%
        0.7
        97.4%
        14.8
        1.0%
        94.7%
        54%
        50 bp
        15.2
        SRX2356930
        2.5%
        0.3
        97.4%
        11.8
        1.1%
        96.2%
        54%
        49 bp
        12.1
        SRX2356931
        1.7%
        0.2
        97.2%
        12.5
        1.1%
        96.2%
        54%
        49 bp
        12.9
        SRX2356932
        1.6%
        0.2
        97.6%
        13.5
        1.4%
        96.2%
        54%
        49 bp
        13.8
        SRX2356933
        5.6%
        0.9
        97.7%
        15.9
        1.1%
        94.4%
        55%
        49 bp
        16.3
        SRX2356934
        7.6%
        1.2
        97.6%
        15.1
        1.2%
        93.1%
        55%
        49 bp
        15.5
        SRX2356935
        7.3%
        0.8
        97.0%
        10.4
        1.1%
        93.2%
        55%
        49 bp
        10.7
        SRX259777
        78.4%
        28.3
        94.7%
        34.2
        19.2%
        69.5%
        55%
        89 bp
        36.2
        SRX259778
        73.8%
        18.0
        94.6%
        23.0
        18.4%
        67.3%
        55%
        90 bp
        24.4
        SRX259779
        53.5%
        13.9
        95.4%
        24.8
        18.5%
        72.0%
        55%
        90 bp
        26.0
        SRX259780
        66.0%
        18.8
        94.9%
        27.0
        18.9%
        70.5%
        55%
        90 bp
        28.5
        SRX259781
        58.8%
        8.7
        94.7%
        14.0
        18.2%
        66.9%
        55%
        91 bp
        14.8
        SRX259782
        60.3%
        8.8
        94.9%
        13.9
        17.2%
        66.4%
        55%
        91 bp
        14.6
        SRX259783
        43.4%
        11.9
        94.8%
        25.9
        20.8%
        74.7%
        55%
        91 bp
        27.4
        SRX259784
        63.8%
        12.1
        94.0%
        17.8
        21.8%
        67.2%
        55%
        91 bp
        18.9
        SRX259785
        25.1%
        5.8
        93.9%
        21.9
        21.3%
        77.5%
        54%
        90 bp
        23.3
        SRX259786
        53.4%
        32.6
        94.0%
        57.3
        25.2%
        78.0%
        55%
        90 bp
        61.0
        SRX259787
        71.0%
        28.7
        93.3%
        37.7
        21.3%
        72.5%
        55%
        91 bp
        40.4
        SRX259788
        51.9%
        26.7
        93.5%
        48.1
        22.4%
        76.7%
        55%
        91 bp
        51.4
        SRX259789
        3.1%
        0.5
        94.2%
        14.5
        11.9%
        86.4%
        54%
        94 bp
        15.4
        SRX259790
        41.1%
        3.8
        93.0%
        8.6
        23.4%
        69.1%
        55%
        94 bp
        9.2
        SRX259791
        52.4%
        15.3
        93.4%
        27.3
        17.8%
        74.9%
        55%
        94 bp
        29.3
        SRX259792
        40.9%
        5.2
        83.7%
        10.7
        37.7%
        71.4%
        54%
        91 bp
        12.8
        SRX259793
        52.9%
        8.2
        87.9%
        13.7
        37.4%
        71.4%
        55%
        93 bp
        15.6
        SRX2769874
        20.1%
        7.9
        99.0%
        39.1
        2.0%
        91.8%
        55%
        35 bp
        39.4
        SRX2769875
        0.2%
        0.0
        3.8%
        0.1
        11.8%
        72.5%
        49%
        48 bp
        1.7
        SRX2769876
        18.4%
        6.5
        98.9%
        35.1
        2.8%
        71.7%
        54%
        35 bp
        35.5
        SRX2769877
        27.3%
        0.4
        94.5%
        1.3
        63.2%
        83.2%
        50%
        31 bp
        1.4
        SRX2769878
        22.2%
        2.0
        94.5%
        8.4
        16.0%
        91.3%
        50%
        34 bp
        8.9
        SRX2769879
        21.1%
        8.6
        99.1%
        40.1
        1.9%
        67.0%
        55%
        35 bp
        40.5
        SRX2769880
        15.0%
        1.9
        64.1%
        8.0
        14.9%
        29.8%
        54%
        32 bp
        12.5
        SRX2769881
        17.5%
        5.1
        75.1%
        21.8
        2.3%
        89.5%
        54%
        35 bp
        29.1
        SRX2769882
        0.1%
        0.0
        1.4%
        0.0
        7.2%
        74.1%
        47%
        49 bp
        1.9
        SRX2769883
        13.5%
        5.5
        98.3%
        40.3
        1.9%
        94.8%
        55%
        35 bp
        41.0
        SRX2769884
        24.0%
        9.6
        99.4%
        39.6
        1.8%
        93.7%
        55%
        35 bp
        39.9
        SRX2769885
        19.9%
        8.2
        99.4%
        40.9
        1.8%
        94.0%
        55%
        35 bp
        41.1
        SRX2769886
        29.6%
        11.6
        99.2%
        39.0
        3.7%
        91.5%
        55%
        35 bp
        39.3
        SRX2769887
        19.8%
        7.4
        98.9%
        36.8
        3.3%
        91.0%
        55%
        35 bp
        37.2
        SRX2769888
        15.9%
        6.2
        99.1%
        38.7
        3.5%
        93.6%
        55%
        35 bp
        39.1
        SRX2769889
        15.5%
        6.0
        98.7%
        38.3
        3.0%
        93.7%
        55%
        35 bp
        38.7
        SRX2769890
        20.5%
        8.0
        98.8%
        38.2
        3.8%
        92.8%
        55%
        35 bp
        38.7
        SRX2769891
        22.2%
        8.6
        98.8%
        38.4
        3.4%
        91.8%
        55%
        35 bp
        38.9
        SRX2769892
        17.5%
        4.7
        98.2%
        26.4
        4.8%
        86.5%
        54%
        35 bp
        26.8
        SRX3159653
        57.7%
        8.6
        90.7%
        13.5
        1.4%
        88.1%
        54%
        49 bp
        14.9
        SRX3159654
        59.3%
        11.1
        89.6%
        16.8
        1.2%
        87.9%
        54%
        49 bp
        18.8
        SRX3159655
        53.4%
        8.9
        91.6%
        15.2
        1.4%
        88.4%
        55%
        49 bp
        16.6
        SRX3159656
        56.7%
        6.1
        90.0%
        9.7
        1.5%
        86.4%
        54%
        49 bp
        10.8
        SRX3159657
        66.8%
        8.2
        92.5%
        11.4
        1.3%
        85.4%
        55%
        49 bp
        12.3
        SRX3159658
        64.4%
        8.9
        93.5%
        12.9
        1.7%
        87.8%
        55%
        49 bp
        13.8
        SRX3159659
        63.4%
        10.7
        92.5%
        15.6
        1.6%
        87.8%
        55%
        49 bp
        16.9
        SRX3159660
        44.7%
        7.4
        95.2%
        15.8
        1.2%
        90.5%
        55%
        49 bp
        16.6
        SRX3159661
        51.7%
        9.3
        76.5%
        13.8
        1.3%
        90.8%
        54%
        49 bp
        18.1
        SRX3159662
        67.4%
        14.3
        87.9%
        18.6
        1.1%
        92.2%
        54%
        50 bp
        21.2
        SRX3159663
        63.6%
        10.9
        84.9%
        14.5
        1.3%
        90.9%
        54%
        49 bp
        17.1
        SRX3159664
        54.7%
        10.6
        80.1%
        15.6
        1.2%
        92.0%
        54%
        49 bp
        19.4
        SRX3159665
        73.5%
        11.8
        92.3%
        14.8
        1.2%
        90.2%
        55%
        49 bp
        16.0
        SRX3159666
        62.4%
        10.8
        83.2%
        14.3
        1.1%
        92.2%
        54%
        50 bp
        17.3
        SRX3159667
        74.0%
        9.9
        92.9%
        12.4
        1.0%
        89.4%
        55%
        50 bp
        13.3
        SRX3159668
        70.6%
        12.0
        90.9%
        15.4
        1.3%
        90.3%
        55%
        49 bp
        17.0
        SRX3172761
        49.3%
        4.7
        88.6%
        8.5
        2.1%
        91.4%
        52%
        49 bp
        9.6
        SRX3172762
        45.9%
        6.1
        89.8%
        11.9
        2.0%
        93.9%
        52%
        49 bp
        13.3
        SRX3172763
        42.2%
        6.4
        88.4%
        13.3
        1.5%
        94.1%
        51%
        49 bp
        15.1
        SRX3172764
        52.6%
        8.9
        91.6%
        15.5
        2.0%
        94.4%
        53%
        49 bp
        16.9
        SRX3172765
        51.5%
        7.2
        91.7%
        12.9
        1.5%
        91.4%
        53%
        49 bp
        14.0
        SRX3172766
        44.4%
        5.8
        89.4%
        11.7
        1.7%
        93.3%
        52%
        49 bp
        13.1
        SRX3176780
        51.7%
        8.6
        80.9%
        13.5
        1.0%
        91.0%
        52%
        50 bp
        16.7
        SRX3176781
        52.3%
        7.9
        83.9%
        12.8
        1.0%
        91.7%
        52%
        50 bp
        15.2
        SRX3176782
        48.1%
        5.2
        80.2%
        8.7
        1.0%
        90.9%
        51%
        50 bp
        10.9
        SRX3176783
        43.5%
        7.5
        82.9%
        14.2
        1.0%
        93.7%
        50%
        50 bp
        17.1
        SRX3176784
        35.5%
        5.2
        78.6%
        11.5
        1.0%
        93.1%
        49%
        50 bp
        14.7
        SRX3176785
        30.9%
        5.2
        85.7%
        14.5
        1.0%
        94.1%
        49%
        50 bp
        16.9
        SRX3176786
        24.4%
        3.1
        82.8%
        10.4
        1.0%
        93.0%
        48%
        50 bp
        12.6
        SRX3176787
        19.2%
        2.4
        83.8%
        10.3
        1.0%
        94.5%
        47%
        50 bp
        12.3
        SRX3176788
        16.8%
        2.6
        84.4%
        13.0
        1.2%
        95.5%
        47%
        50 bp
        15.4
        SRX3176789
        67.0%
        7.3
        90.3%
        9.8
        1.0%
        86.5%
        54%
        50 bp
        10.9
        SRX3176790
        67.7%
        10.6
        91.0%
        14.3
        1.0%
        89.5%
        54%
        50 bp
        15.7
        SRX3176791
        67.8%
        7.9
        91.5%
        10.6
        1.4%
        88.4%
        54%
        49 bp
        11.6
        SRX3176792
        64.7%
        6.5
        89.8%
        9.0
        1.2%
        87.2%
        54%
        49 bp
        10.0
        SRX3176793
        60.0%
        8.2
        87.0%
        11.9
        1.2%
        88.9%
        53%
        49 bp
        13.7
        SRX3176794
        60.6%
        10.7
        90.6%
        16.0
        1.1%
        89.9%
        53%
        50 bp
        17.6
        SRX3176795
        51.9%
        7.2
        85.8%
        11.9
        1.0%
        90.1%
        52%
        50 bp
        13.9
        SRX3176796
        41.5%
        8.9
        81.8%
        17.6
        1.2%
        94.2%
        51%
        50 bp
        21.5
        SRX3176797
        2.2%
        0.3
        49.5%
        7.6
        1.0%
        93.9%
        52%
        50 bp
        15.4
        SRX3176798
        61.8%
        5.6
        91.2%
        8.2
        1.2%
        84.8%
        54%
        49 bp
        9.0
        SRX3176799
        54.1%
        4.5
        90.6%
        7.5
        1.2%
        86.4%
        53%
        49 bp
        8.3
        SRX3176800
        51.5%
        4.8
        91.5%
        8.4
        1.1%
        88.3%
        52%
        49 bp
        9.2
        SRX3176801
        41.9%
        3.8
        92.2%
        8.3
        2.1%
        92.4%
        52%
        49 bp
        9.0
        SRX3176802
        34.9%
        2.7
        92.1%
        7.0
        1.6%
        92.6%
        50%
        49 bp
        7.6
        SRX3176803
        29.3%
        2.3
        92.2%
        7.3
        1.1%
        90.1%
        50%
        49 bp
        7.9
        SRX3176804
        19.1%
        2.3
        93.3%
        11.1
        1.5%
        94.9%
        48%
        49 bp
        11.9
        SRX3176805
        20.6%
        2.2
        93.0%
        9.9
        1.3%
        93.2%
        48%
        49 bp
        10.6
        SRX3176806
        13.1%
        1.0
        95.6%
        7.5
        1.4%
        92.8%
        51%
        49 bp
        7.9
        SRX3176807
        74.3%
        7.7
        95.0%
        9.9
        1.8%
        89.5%
        55%
        49 bp
        10.4
        SRX3176808
        71.5%
        9.1
        94.5%
        12.0
        2.5%
        90.5%
        55%
        49 bp
        12.7
        SRX3176809
        70.8%
        8.0
        94.1%
        10.7
        2.0%
        89.7%
        54%
        49 bp
        11.4
        SRX3176810
        62.2%
        13.5
        91.9%
        19.9
        1.5%
        93.2%
        53%
        49 bp
        21.7
        SRX3176811
        4.8%
        0.7
        94.2%
        12.8
        4.5%
        91.6%
        54%
        49 bp
        13.6
        SRX3176812
        5.5%
        1.2
        93.1%
        21.3
        2.2%
        93.3%
        53%
        49 bp
        22.9
        SRX3176813
        6.5%
        0.8
        94.9%
        11.9
        2.3%
        92.5%
        53%
        49 bp
        12.6
        SRX3176814
        5.9%
        0.7
        94.7%
        11.8
        1.6%
        95.0%
        52%
        49 bp
        12.4
        SRX3176815
        3.5%
        0.5
        89.9%
        12.3
        1.7%
        96.0%
        49%
        49 bp
        13.7
        SRX3211301
        76.6%
        6.0
        98.0%
        7.7
        0.9%
        81.6%
        56%
        50 bp
        7.9
        SRX3211302
        75.6%
        6.3
        97.9%
        8.2
        1.1%
        95.3%
        55%
        49 bp
        8.4
        SRX3211303
        74.3%
        5.9
        98.2%
        7.8
        0.9%
        83.5%
        55%
        50 bp
        8.0
        SRX3211304
        71.6%
        6.4
        98.9%
        8.8
        0.9%
        95.7%
        55%
        50 bp
        8.9
        SRX3211305
        72.3%
        7.6
        97.8%
        10.3
        1.3%
        89.4%
        56%
        50 bp
        10.5
        SRX3211306
        73.9%
        5.7
        99.1%
        7.6
        1.0%
        95.2%
        55%
        50 bp
        7.7
        SRX3211307
        75.7%
        8.0
        98.8%
        10.4
        0.9%
        85.8%
        55%
        50 bp
        10.5
        SRX3211308
        69.0%
        6.3
        98.8%
        9.0
        1.1%
        96.3%
        54%
        49 bp
        9.1
        SRX3211309
        75.6%
        6.9
        98.6%
        9.0
        1.0%
        84.2%
        55%
        50 bp
        9.1
        SRX3211310
        69.8%
        5.2
        98.9%
        7.4
        1.2%
        94.6%
        55%
        49 bp
        7.5
        SRX3211311
        76.5%
        7.6
        98.5%
        9.7
        0.9%
        85.8%
        55%
        50 bp
        9.9
        SRX3211312
        71.5%
        5.4
        99.0%
        7.5
        1.3%
        95.2%
        55%
        49 bp
        7.6
        SRX3211313
        73.4%
        6.9
        98.2%
        9.3
        0.9%
        86.0%
        55%
        50 bp
        9.4
        SRX3211314
        70.6%
        6.7
        98.4%
        9.3
        1.3%
        95.8%
        54%
        49 bp
        9.4
        SRX3211315
        74.4%
        8.5
        98.4%
        11.3
        1.0%
        87.7%
        55%
        50 bp
        11.5
        SRX3211316
        72.1%
        7.8
        98.7%
        10.7
        1.7%
        96.4%
        54%
        49 bp
        10.8
        SRX3211317
        72.1%
        9.3
        98.4%
        12.6
        0.9%
        86.8%
        55%
        50 bp
        12.8
        SRX3211318
        73.0%
        7.3
        99.0%
        9.9
        1.3%
        96.0%
        55%
        49 bp
        10.0
        SRX3211319
        73.5%
        9.7
        98.7%
        13.0
        0.9%
        92.7%
        56%
        50 bp
        13.2
        SRX3211320
        70.4%
        6.4
        98.6%
        9.0
        1.6%
        95.9%
        55%
        49 bp
        9.1
        SRX3211321
        75.1%
        5.6
        98.2%
        7.3
        0.9%
        79.5%
        55%
        50 bp
        7.5
        SRX3211322
        73.0%
        8.0
        98.5%
        10.8
        1.1%
        96.4%
        55%
        50 bp
        11.0
        SRX3211323
        77.5%
        4.5
        98.5%
        5.8
        0.9%
        79.6%
        56%
        50 bp
        5.8
        SRX3211324
        77.7%
        3.4
        98.8%
        4.3
        1.1%
        92.8%
        56%
        50 bp
        4.4
        SRX3211325
        80.3%
        5.0
        99.0%
        6.1
        1.0%
        79.1%
        56%
        50 bp
        6.2
        SRX3211326
        50.2%
        4.6
        98.6%
        9.1
        1.1%
        96.4%
        56%
        49 bp
        9.3
        SRX3211327
        79.5%
        6.0
        98.9%
        7.4
        0.9%
        82.8%
        56%
        50 bp
        7.5
        SRX3211328
        40.1%
        3.4
        99.0%
        8.3
        0.9%
        97.3%
        55%
        50 bp
        8.4
        SRX3211329
        78.0%
        4.8
        98.5%
        6.1
        0.9%
        80.2%
        55%
        50 bp
        6.2
        SRX3211330
        74.4%
        4.0
        98.3%
        5.2
        1.1%
        93.6%
        55%
        50 bp
        5.3
        SRX3211331
        76.7%
        4.6
        98.2%
        5.9
        0.9%
        79.2%
        55%
        50 bp
        6.0
        SRX3211332
        73.7%
        5.6
        98.4%
        7.5
        1.3%
        96.1%
        55%
        50 bp
        7.6
        SRX3211333
        74.8%
        4.8
        98.2%
        6.3
        0.9%
        79.8%
        55%
        50 bp
        6.4
        SRX3211334
        60.1%
        4.9
        97.8%
        8.0
        1.2%
        96.4%
        53%
        49 bp
        8.1
        SRX3211335
        58.3%
        4.1
        98.3%
        6.9
        1.0%
        83.6%
        53%
        50 bp
        7.0
        SRX3211336
        70.4%
        4.7
        98.0%
        6.5
        1.3%
        94.3%
        54%
        49 bp
        6.7
        SRX3211337
        72.5%
        5.2
        97.9%
        7.0
        0.9%
        81.4%
        55%
        50 bp
        7.2
        SRX3211338
        71.2%
        6.9
        97.8%
        9.5
        1.0%
        95.5%
        55%
        50 bp
        9.7
        SRX3211339
        75.5%
        6.5
        97.9%
        8.4
        0.9%
        81.5%
        56%
        50 bp
        8.6
        SRX3211340
        77.4%
        6.6
        97.8%
        8.3
        1.1%
        94.6%
        56%
        50 bp
        8.5
        SRX3211341
        76.9%
        7.4
        98.0%
        9.4
        0.9%
        82.7%
        56%
        50 bp
        9.6
        SRX3211342
        75.7%
        6.2
        97.9%
        8.1
        1.1%
        94.3%
        56%
        50 bp
        8.2
        SRX3211343
        68.9%
        6.4
        97.9%
        9.1
        1.0%
        96.3%
        54%
        50 bp
        9.3
        SRX3211344
        73.1%
        3.8
        98.1%
        5.1
        1.0%
        79.5%
        55%
        50 bp
        5.2
        SRX3211345
        69.5%
        6.2
        97.4%
        8.7
        1.2%
        95.2%
        55%
        50 bp
        8.9
        SRX3211346
        73.2%
        6.4
        98.0%
        8.6
        0.9%
        83.0%
        55%
        50 bp
        8.8
        SRX3211347
        55.3%
        4.4
        98.2%
        7.9
        1.0%
        96.3%
        55%
        50 bp
        8.0
        SRX3211348
        78.3%
        6.6
        98.5%
        8.4
        0.9%
        81.1%
        56%
        50 bp
        8.5
        SRX3211349
        69.3%
        7.3
        97.8%
        10.3
        1.0%
        96.7%
        54%
        50 bp
        10.5
        SRX3211350
        73.2%
        5.8
        98.5%
        7.8
        0.9%
        83.6%
        55%
        50 bp
        7.9
        SRX3211351
        48.9%
        3.5
        98.3%
        7.0
        1.1%
        96.5%
        55%
        50 bp
        7.1
        SRX3211352
        67.0%
        4.9
        97.8%
        7.2
        0.9%
        84.2%
        54%
        50 bp
        7.3
        SRX3211353
        61.7%
        5.3
        97.3%
        8.3
        1.3%
        95.5%
        54%
        49 bp
        8.6
        SRX3211354
        62.5%
        4.6
        98.2%
        7.2
        1.0%
        82.7%
        54%
        50 bp
        7.4
        SRX3211355
        67.5%
        5.1
        97.3%
        7.4
        1.7%
        94.5%
        55%
        49 bp
        7.6
        SRX3211356
        71.4%
        4.6
        97.8%
        6.3
        1.0%
        75.8%
        55%
        50 bp
        6.4
        SRX3211357
        69.9%
        5.8
        97.6%
        8.1
        1.3%
        96.0%
        55%
        50 bp
        8.3
        SRX3211358
        74.4%
        5.9
        97.9%
        7.8
        0.9%
        79.6%
        55%
        50 bp
        8.0
        SRX3211359
        70.5%
        6.7
        97.7%
        9.3
        1.3%
        96.0%
        55%
        50 bp
        9.5
        SRX3211360
        73.7%
        6.1
        98.1%
        8.1
        0.9%
        82.1%
        55%
        50 bp
        8.2
        SRX3312459
        66.8%
        7.9
        88.7%
        10.5
        1.2%
        86.5%
        54%
        49 bp
        11.9
        SRX3312460
        68.3%
        7.9
        90.3%
        10.4
        1.0%
        87.6%
        54%
        50 bp
        11.5
        SRX3312461
        65.9%
        9.1
        89.6%
        12.3
        1.1%
        90.0%
        54%
        49 bp
        13.7
        SRX3312462
        63.3%
        8.2
        89.6%
        11.6
        1.0%
        89.1%
        53%
        50 bp
        12.9
        SRX3312463
        58.4%
        7.7
        88.8%
        11.8
        1.1%
        89.5%
        53%
        50 bp
        13.3
        SRX3312464
        58.6%
        10.0
        90.3%
        15.5
        1.1%
        91.7%
        52%
        50 bp
        17.1
        SRX3312465
        50.7%
        5.9
        87.5%
        10.2
        1.2%
        87.7%
        52%
        50 bp
        11.7
        SRX3312466
        45.5%
        4.2
        87.3%
        8.1
        1.1%
        88.9%
        51%
        50 bp
        9.3
        SRX3312467
        38.4%
        4.6
        86.5%
        10.4
        1.1%
        91.0%
        51%
        50 bp
        12.0
        SRX3312468
        56.4%
        6.1
        80.8%
        8.7
        1.0%
        87.7%
        54%
        50 bp
        10.8
        SRX3312469
        60.7%
        7.6
        85.9%
        10.8
        1.0%
        87.9%
        54%
        50 bp
        12.6
        SRX3312470
        61.4%
        15.8
        88.5%
        22.8
        1.0%
        93.1%
        54%
        50 bp
        25.8
        SRX3312471
        53.8%
        9.2
        83.5%
        14.3
        1.2%
        90.9%
        54%
        50 bp
        17.2
        SRX3312472
        53.9%
        9.4
        85.8%
        15.0
        1.6%
        90.6%
        54%
        49 bp
        17.5
        SRX3312473
        45.6%
        6.5
        83.8%
        11.9
        1.5%
        88.9%
        54%
        49 bp
        14.2
        SRX3312474
        6.2%
        0.7
        88.2%
        10.2
        2.5%
        91.8%
        53%
        49 bp
        11.6
        SRX3312475
        5.4%
        0.7
        81.5%
        10.9
        1.2%
        92.5%
        52%
        49 bp
        13.4
        SRX3312476
        4.2%
        0.5
        82.6%
        9.4
        1.3%
        93.2%
        52%
        49 bp
        11.3
        SRX3312477
        62.6%
        3.6
        86.9%
        4.9
        1.8%
        83.2%
        54%
        49 bp
        5.7
        SRX3312478
        52.2%
        3.8
        89.4%
        6.5
        1.9%
        85.7%
        54%
        49 bp
        7.3
        SRX3312479
        62.2%
        5.3
        90.4%
        7.8
        2.1%
        86.6%
        54%
        49 bp
        8.6
        SRX3312480
        62.9%
        5.5
        89.9%
        7.9
        2.7%
        91.5%
        54%
        49 bp
        8.8
        SRX3312481
        58.4%
        5.8
        89.2%
        8.8
        1.3%
        85.9%
        53%
        49 bp
        9.9
        SRX3312482
        50.3%
        3.5
        82.8%
        5.8
        2.6%
        87.9%
        52%
        49 bp
        7.0
        SRX3312483
        52.5%
        4.8
        91.6%
        8.4
        1.7%
        89.6%
        52%
        49 bp
        9.2
        SRX3312484
        50.2%
        4.8
        88.6%
        8.4
        2.0%
        88.6%
        52%
        49 bp
        9.5
        SRX3312485
        44.4%
        4.9
        90.9%
        10.1
        2.2%
        88.9%
        52%
        49 bp
        11.1
        SRX3312486
        57.1%
        5.8
        89.0%
        9.0
        1.9%
        89.4%
        55%
        49 bp
        10.1
        SRX3312487
        60.6%
        5.1
        89.8%
        7.5
        2.9%
        85.4%
        55%
        49 bp
        8.4
        SRX3312488
        60.7%
        6.0
        89.0%
        8.8
        1.4%
        89.8%
        55%
        49 bp
        9.9
        SRX3312489
        56.0%
        4.4
        86.6%
        6.8
        1.1%
        89.3%
        54%
        50 bp
        7.9
        SRX3312490
        42.7%
        4.0
        78.8%
        7.3
        1.3%
        90.4%
        54%
        50 bp
        9.3
        SRX3312491
        48.4%
        1.6
        87.1%
        3.0
        1.8%
        82.9%
        54%
        49 bp
        3.4
        SRX3312492
        5.9%
        1.4
        90.4%
        20.7
        1.4%
        92.9%
        53%
        49 bp
        22.9
        SRX3312493
        4.8%
        0.5
        85.7%
        9.0
        1.4%
        92.4%
        53%
        49 bp
        10.5
        SRX3312494
        5.1%
        0.3
        86.5%
        5.3
        1.8%
        91.9%
        52%
        49 bp
        6.2
        SRX359366
        9.1%
        1.2
        98.4%
        13.4
        1.1%
        95.3%
        54%
        50 bp
        13.7
        SRX359367
        9.6%
        1.2
        98.5%
        11.8
        0.9%
        95.5%
        54%
        51 bp
        12.0
        SRX359368
        8.1%
        1.0
        98.1%
        11.7
        0.8%
        95.5%
        54%
        51 bp
        11.9
        SRX359369
        9.1%
        1.3
        98.1%
        13.9
        0.8%
        95.5%
        54%
        51 bp
        14.2
        SRX359370
        10.1%
        1.2
        98.5%
        11.3
        0.9%
        94.9%
        54%
        51 bp
        11.5
        SRX359371
        9.5%
        1.2
        98.2%
        12.0
        0.8%
        95.2%
        54%
        51 bp
        12.2
        SRX359372
        6.8%
        0.7
        99.3%
        9.5
        0.8%
        95.8%
        54%
        51 bp
        9.6
        SRX359373
        6.6%
        0.8
        99.2%
        11.5
        0.8%
        96.1%
        54%
        51 bp
        11.6
        SRX359374
        6.2%
        0.8
        99.1%
        12.5
        0.8%
        96.2%
        54%
        51 bp
        12.7
        SRX359375
        5.7%
        0.7
        99.1%
        11.7
        0.7%
        96.4%
        54%
        51 bp
        11.8
        SRX359376
        6.0%
        0.6
        99.2%
        10.4
        0.8%
        95.7%
        54%
        51 bp
        10.5
        SRX359377
        5.4%
        0.6
        99.3%
        11.5
        0.8%
        96.3%
        54%
        51 bp
        11.6
        SRX359378
        7.4%
        0.8
        99.2%
        10.2
        0.9%
        95.7%
        54%
        51 bp
        10.3
        SRX359379
        6.7%
        0.6
        99.2%
        9.5
        0.8%
        95.8%
        54%
        51 bp
        9.5
        SRX359380
        5.7%
        0.6
        99.1%
        10.3
        1.0%
        96.1%
        54%
        51 bp
        10.4
        SRX359381
        7.8%
        0.8
        99.3%
        9.9
        0.8%
        95.7%
        54%
        51 bp
        10.0
        SRX359382
        8.0%
        1.0
        99.2%
        12.1
        0.9%
        95.7%
        54%
        51 bp
        12.2
        SRX359383
        7.7%
        0.9
        99.2%
        12.1
        0.9%
        95.9%
        54%
        51 bp
        12.2
        SRX4105497
        16.5%
        2.2
        43.2%
        5.9
        1.4%
        90.7%
        54%
        49 bp
        13.5
        SRX4105498
        7.1%
        1.3
        30.9%
        5.6
        1.2%
        94.1%
        54%
        49 bp
        18.1
        SRX4105499
        6.4%
        0.8
        34.5%
        4.4
        1.2%
        93.7%
        54%
        49 bp
        12.7
        SRX4105500
        1.9%
        0.5
        7.8%
        2.2
        1.4%
        96.5%
        54%
        49 bp
        28.7
        SRX4105501
        7.4%
        1.0
        33.0%
        4.3
        1.3%
        93.4%
        54%
        49 bp
        12.9
        SRX4105502
        4.8%
        1.0
        32.6%
        6.7
        1.4%
        96.5%
        54%
        49 bp
        20.6
        SRX4105503
        16.3%
        3.4
        43.3%
        9.1
        1.4%
        91.6%
        54%
        49 bp
        20.9
        SRX4105504
        7.5%
        1.4
        31.4%
        5.7
        1.4%
        93.6%
        54%
        49 bp
        18.2
        SRX4105505
        6.2%
        0.9
        33.8%
        4.9
        1.3%
        93.9%
        54%
        49 bp
        14.4
        SRX4105506
        0.4%
        0.0
        4.0%
        0.2
        10.4%
        97.3%
        54%
        50 bp
        4.5
        SRX4105507
        0.4%
        0.0
        3.9%
        0.2
        11.8%
        96.8%
        54%
        50 bp
        3.9
        SRX4105508
        1.9%
        0.2
        7.8%
        0.9
        1.4%
        95.0%
        54%
        49 bp
        11.3
        SRX4105509
        7.4%
        0.8
        33.4%
        3.6
        1.3%
        93.0%
        54%
        49 bp
        10.8
        SRX4105510
        5.7%
        0.9
        33.8%
        5.5
        1.2%
        95.1%
        54%
        49 bp
        16.3
        SRX4105511
        42.6%
        1.4
        82.5%
        2.7
        0.7%
        76.8%
        54%
        73 bp
        3.3
        SRX4105512
        56.4%
        2.5
        84.5%
        3.8
        0.7%
        72.0%
        56%
        73 bp
        4.5
        SRX4105513
        18.8%
        0.8
        45.0%
        1.8
        0.3%
        83.1%
        55%
        73 bp
        4.1
        SRX4105514
        32.9%
        1.7
        67.8%
        3.5
        0.3%
        78.8%
        55%
        73 bp
        5.1
        SRX4105515
        4.1%
        0.1
        27.4%
        1.0
        0.3%
        88.0%
        55%
        73 bp
        3.5
        SRX4105516
        26.6%
        1.3
        55.1%
        2.6
        0.3%
        81.1%
        55%
        73 bp
        4.8
        SRX4105517
        1.8%
        0.3
        11.2%
        2.1
        2.3%
        94.5%
        54%
        49 bp
        18.3
        SRX4105518
        3.4%
        0.5
        27.2%
        4.0
        4.7%
        97.7%
        53%
        50 bp
        14.6
        SRX4105519
        4.2%
        0.1
        25.3%
        0.6
        3.3%
        96.7%
        54%
        50 bp
        2.4
        SRX4105520
        1.2%
        0.2
        9.4%
        1.3
        2.1%
        94.6%
        54%
        49 bp
        13.6
        SRX4105521
        0.8%
        0.1
        8.3%
        0.8
        2.3%
        94.2%
        54%
        49 bp
        9.7
        SRX4105522
        4.8%
        0.9
        19.3%
        3.4
        2.2%
        93.0%
        54%
        49 bp
        17.8
        SRX4105523
        1.2%
        0.1
        9.7%
        1.1
        2.2%
        94.1%
        54%
        49 bp
        11.0
        SRX4105524
        0.6%
        0.1
        6.5%
        0.9
        2.2%
        95.7%
        54%
        49 bp
        13.3
        SRX4105525
        17.3%
        2.1
        75.0%
        9.2
        1.4%
        90.6%
        52%
        49 bp
        12.3
        SRX4105526
        48.0%
        10.4
        76.8%
        16.7
        1.8%
        85.1%
        55%
        49 bp
        21.7
        SRX4105527
        39.4%
        7.0
        83.2%
        14.8
        1.2%
        87.4%
        55%
        49 bp
        17.8
        SRX4105528
        41.8%
        7.2
        74.9%
        13.0
        1.3%
        86.1%
        55%
        49 bp
        17.3
        SRX4105529
        53.3%
        11.1
        82.6%
        17.2
        1.3%
        87.1%
        55%
        49 bp
        20.9
        SRX4105530
        59.9%
        14.6
        88.6%
        21.6
        1.6%
        92.3%
        55%
        49 bp
        24.4
        SRX4105531
        0.8%
        0.0
        7.2%
        0.4
        3.7%
        96.9%
        54%
        50 bp
        5.2
        SRX4105532
        0.8%
        0.0
        7.0%
        0.2
        4.2%
        95.5%
        54%
        50 bp
        3.1
        SRX4105533
        17.2%
        2.8
        76.0%
        12.3
        1.6%
        91.8%
        52%
        49 bp
        16.2
        SRX4105534
        6.3%
        0.5
        27.2%
        2.1
        7.7%
        97.9%
        54%
        49 bp
        7.7
        SRX4105535
        6.3%
        0.4
        26.9%
        1.8
        8.5%
        97.6%
        54%
        49 bp
        6.7
        SRX4105536
        38.9%
        6.1
        83.1%
        12.9
        1.3%
        86.5%
        55%
        49 bp
        15.6
        SRX4105537
        41.7%
        3.8
        75.1%
        6.8
        1.3%
        82.5%
        55%
        49 bp
        9.1
        SRX4105538
        54.6%
        10.1
        82.9%
        15.3
        1.2%
        84.5%
        55%
        49 bp
        18.4
        SRX4105539
        58.8%
        7.1
        88.2%
        10.6
        1.5%
        86.3%
        54%
        49 bp
        12.0
        SRX4105540
        38.4%
        6.8
        59.7%
        10.5
        4.8%
        94.3%
        52%
        49 bp
        17.6
        SRX4105541
        54.1%
        0.5
        83.5%
        0.7
        10.8%
        69.1%
        58%
        72 bp
        0.8
        SRX4105542
        56.4%
        1.7
        95.9%
        2.9
        1.7%
        68.7%
        56%
        73 bp
        3.0
        SRX4105543
        71.1%
        1.9
        94.9%
        2.6
        6.7%
        72.0%
        57%
        73 bp
        2.7
        SRX4105544
        75.2%
        1.9
        96.0%
        2.4
        2.1%
        67.1%
        56%
        73 bp
        2.5
        SRX4105545
        73.1%
        2.4
        95.0%
        3.2
        1.0%
        67.8%
        57%
        73 bp
        3.3
        SRX4105546
        68.7%
        2.2
        94.5%
        3.0
        1.5%
        68.2%
        57%
        73 bp
        3.2
        SRX4105547
        2.1%
        0.3
        10.9%
        1.6
        2.2%
        94.3%
        54%
        49 bp
        14.5
        SRX4105548
        2.9%
        0.5
        15.8%
        2.7
        2.1%
        93.7%
        54%
        49 bp
        17.1
        SRX4105549
        5.6%
        0.5
        25.8%
        2.2
        3.1%
        98.0%
        54%
        50 bp
        8.4
        SRX4105550
        2.4%
        0.3
        16.1%
        2.2
        2.2%
        94.1%
        54%
        49 bp
        13.7
        SRX4105551
        14.9%
        0.7
        44.8%
        2.0
        3.7%
        96.2%
        54%
        50 bp
        4.5
        SRX4105552
        6.0%
        1.0
        27.5%
        4.5
        2.1%
        91.9%
        54%
        49 bp
        16.4
        SRX4105553
        2.7%
        0.4
        19.3%
        2.8
        2.2%
        94.0%
        54%
        49 bp
        14.5
        SRX4105554
        3.4%
        0.4
        16.6%
        2.2
        2.3%
        93.3%
        55%
        49 bp
        13.1
        SRX4105555
        66.0%
        2.2
        94.4%
        3.2
        4.5%
        75.4%
        56%
        73 bp
        3.4
        SRX4105556
        66.6%
        0.5
        87.2%
        0.7
        13.5%
        57.0%
        59%
        72 bp
        0.8
        SRX4105557
        72.6%
        2.5
        95.8%
        3.3
        0.4%
        67.9%
        56%
        73 bp
        3.4
        SRX4105558
        71.1%
        1.8
        92.8%
        2.4
        0.8%
        65.0%
        56%
        73 bp
        2.6
        SRX4105559
        65.7%
        2.0
        93.3%
        2.9
        4.4%
        71.4%
        57%
        73 bp
        3.1
        SRX4105560
        54.0%
        1.3
        75.5%
        1.8
        9.8%
        74.7%
        64%
        71 bp
        2.4
        SRX4105561
        5.0%
        0.7
        21.3%
        3.0
        3.4%
        92.2%
        55%
        49 bp
        14.0
        SRX4105562
        2.2%
        0.3
        15.0%
        1.8
        2.3%
        93.6%
        54%
        49 bp
        12.1
        SRX4105563
        6.4%
        0.8
        26.8%
        3.5
        2.1%
        91.7%
        54%
        49 bp
        13.2
        SRX4105564
        10.8%
        1.1
        42.6%
        4.5
        2.5%
        88.8%
        54%
        49 bp
        10.6
        SRX4105565
        31.2%
        4.1
        68.1%
        9.0
        4.8%
        85.3%
        55%
        49 bp
        13.2
        SRX4105566
        7.2%
        1.1
        26.5%
        3.9
        2.6%
        91.1%
        54%
        49 bp
        14.7
        SRX4105567
        2.6%
        0.3
        12.9%
        1.7
        3.0%
        93.2%
        55%
        49 bp
        13.1
        SRX4105568
        5.0%
        0.7
        21.3%
        3.2
        3.4%
        92.3%
        54%
        49 bp
        15.0
        SRX5055969
        26.5%
        3.0
        46.4%
        5.2
        13.9%
        71.9%
        55%
        88 bp
        11.3
        SRX5055970
        23.0%
        2.5
        46.1%
        5.0
        18.1%
        67.1%
        55%
        86 bp
        10.9
        SRX5055971
        23.0%
        2.5
        47.2%
        5.2
        16.3%
        60.1%
        56%
        87 bp
        10.9
        SRX5055972
        28.0%
        2.7
        45.2%
        4.4
        12.4%
        62.1%
        54%
        90 bp
        9.7
        SRX689242
        28.8%
        0.3
        78.4%
        0.9
        4.3%
        83.5%
        53%
        50 bp
        1.1
        SRX7119038
        26.5%
        3.0
        46.4%
        5.2
        14.4%
        71.9%
        55%
        88 bp
        11.3
        SRX7119039
        23.0%
        2.5
        46.1%
        5.0
        18.1%
        67.1%
        55%
        86 bp
        10.9
        SRX7119040
        19.6%
        1.8
        45.3%
        4.3
        18.0%
        63.7%
        56%
        86 bp
        9.4
        SRX7119041
        27.8%
        3.1
        46.5%
        5.2
        12.4%
        61.8%
        54%
        91 bp
        11.1
        SRX8650808
        65.8%
        28.5
        93.9%
        40.7
        0.1%
        85.9%
        54%
        75 bp
        43.3

        featureCounts

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Bowtie 1

        Bowtie 1 is an ultrafast, memory-efficient short read aligner.

        This plot shows the number of reads aligning to the reference in different ways.

        There are 3 possible types of alignment: * Aligned: Read has only one occurence in the reference genome. * Multimapped: Read has multiple occurence. * Not aligned: Read has no occurence.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        RSeQC

        RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

        Infer experiment

        Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Trimmed Sequence Lengths

        This plot shows the number of reads with certain lengths of adapter trimmed.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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